Fungal Taxonomy

By Ann Atkinson, EMLab Northeast Laboratory Manager

Fungal taxonomy is essentially the process of naming a fungus. Fungi are named according to a binomial system of nomenclature (the names or terms comprising a set or system) using the genus and species name. The names of the fungi are recorded in the International Code of Botanical Nomenclature. With hundreds of thousands of known fungal species and many more yet to be discovered and named fungal taxonomy is a challenge. Add the fact that many fungi have a sexual stage (teleomorph), an asexual stage (anamorph), some fungi are dimorphic - having yeast and mycelial phases, and some fungi may display several types of independently propagating anamorphs (synanamorphs), all of which may have their own names. Well, you can see how some confusion may arise. The same fungus may have been given several names depending on the stage of growth observed. Aspergillus and Eurotium are a good example, where Aspergillus is the asexual stage and Eurotium the sexual stage of the same fungus.

Historically, classification is based on macroscopically and microscopically observable characteristics - the phenotypic approach. The color of the growth, rate of growth, method of spore production, and hyphal septation all aid in assigning a fungus a name. More recently newer technologies have aided both in identifying new organisms and recognizing the various forms of the same organism. Electron microscopy allows recognition of structures not visible by light microscopy. Physiological and biochemical techniques are being applied as well as identification of secondary metabolites. Polymerase Chain Reaction (PCR) allows comparison of the DNA or RNA structure of organisms, including fungi. Selection of universal oligonucleotide (a chain of few neucleotides) primers specific to fungi has provided access to nucleotide sequencing. Electrophoretic (sorting proteins according to their responses to their electric field) methods have been useful in studying Penicillium, Fusarium and Trichoderma.

At present, the majority of fungal identification in environmental labs is based on macroscopic and microscopic features. Features that separate the major groups of fungi are as follows:

Oomycetes:This group consists of the water molds and sexual reproduction is by oogonia, eggs, and motile sperm. Asexually they produce zoospores. The hyphae have no or few septa (crossed walls which separate individual cells in hyphae). Because of their motile zoospores, they require water for reproduction and are often encountered in wet soil or water. They are root and fish pathogens and are rarely seen on spore trap slides.

Zygomycetes:This group consists of microfungi such as Rhizopus and Mucor. They reproduce sexually by cellular fusion and the production of resistant zygospores. Asexually, they produce spores in enclosed sporangia (sporangiospores). Their hyphae usually lack septa. This group is commonly encountered in the soil and only occasionally in water. While spores of Rhizopus may be identifiable on spore trap slides the others such as Mucor are more difficult and must be cultured for identification.

Ascomycetes:This group consists of yeasts, cup fungi, morels and plant pathogens. They reproduce sexually by cellular and nuclear fusion and form ascospores produced inside an ascus (a sac in ascomycetes in which sexual spores are formed). Asexual reproduction is by conidia, which are produced on a phenomenal range of different kinds of structures. The form of these structures and the way the spores are produced are used in the naming of these fungi. The hyphae have numerous septa. They are generally inhabitants of soil but may be found in freshwater and marine habitats. Both sexual and asexual spores are abundant in air. Most of the fungi that are common indoors are asexual stages of Ascomycetes. Some of these are readily identified on spore trap slides. Others require culture and examination of spore bearing structures for identification.

It should be noted that, because so many asexual ascomycete forms are common, classification systems have arisen based on the morphology of these forms. This is the source of much naming confusion in fungal taxonomy. Some of the group names that have been applied to asexual fungi are Hyphomycetes, Coelomycetes, Deuteromycetes, and Fungi Imperfecti.

Basidiomycetes:This group consists of some yeasts, rusts, smuts, jelly fungi, puffballs, mushrooms, boletes and shelf fungi. They reproduce by means of cellular fusion which may occur long before nuclear fusion and spore formation. They produce basidiospores externally on basidia. Asexual spores are conidia. Basidiomycetes have hyphae with septa. The hyphae of many basidiomycetes form tiny tubes that connect one cell to the next, allowing migration of nuclei. These are called clamp connections. Basidiomycetes grow in soil, producing above-ground fruiting bodies on which spores are formed. Spores of many Basidiomycetes are abundant in air and some can be identified microscopically.

A very few fungi have common names, and most of these describe macroscopic fruiting bodies (e.g., Witch's butter or yellow brain fungus for Tremella mesenterica, which is an orange yellow, gelatinous fungus of irregular brain like shape found on dead wood). Some of the common fungi found indoors have names derived from their plant hosts. Thus some Penicillium species produce "Blue Mold" and members of one group of Ascomycetes are called "Powdery Mildews."

Finally, did you know that the very common fungus Aspergillus niger produces the primary ingredient in BEANO???

Microorganism of the Month: Corynebacterium species

By Karen A. Santo-Pietro, EMLab Analyst

The Corynebacterium genus includes a variable group of bacteria that have been isolated from animals (skin, feces, and milk), plants (vegetables and fruits), and soil. Some species have been used in the industrial production of amino acids such as lysine. Thirty one species are of medical importance to humans.

Corynebacterium cells typically appear under the microscope as straight or slightly curved thin rods with swollen or club-like ends (Figure 1). The genus name is taken from the Greek word "koryne" which means "club." The cells may be single rods or in pairs. The rods tend to give rise to rods that are partially fused to the mother cell. Consequently, the bacteria look like the letters "V" or "L." They may also be found in parallel arrangements of rods, called "palisades." They are non-motile (lack the ability to move of their own accord) and do not form branches or spores.

Corynebacterium spp. are Gram-positive (Figure 1). In the Gram staining test, they retain the crystal violet color after washing with alcohol and appear dark purple. They may stain unevenly leading to a beaded appearance. The organisms are facultative aerobes, which means they can grow with or without molecular oxygen (O2). In the laboratory, cultures can grow in ambient air or may be incubated in a 5-10% CO2-enriched environment. Corynebacterium spp. need nutritionally rich media such as serum or blood media for ideal growth. They do not grow on MacConkey agar. The species that are associated with human diseases all grow at 37°C (body temperature). The rest can be grown at room temperature (e.g., species that are part of the normal skin flora). The bacteria grow into convex and semi-opaque colonies, with a mat-textured surface (Figure 2). Colony color may be white, pale tan, or cream. Some species, such as C. diphtheriae, when grown on special media (such as Tinsdale with agar) may appear as black colonies with a brown to gray halo. The Corynebacterium spp. are difficult to identify to genus and species level and would need extensive biochemical testing to get a positive identification.

Most species of Corynebacterium do not cause disease. In humans, they are usually part of the normal skin and mucous membrane flora. Consequently, these common species may be found in the indoor environment or wherever human skin is shed. Rarely, some species may opportunistically infect elderly and immunocompromised individuals. They may cause infections of the urinary tract, throat (pharyngitis), blood (granulomatous lymphadenitis), lungs (pneumonitis), wounds/skin, and the heart (endocarditis). Endocarditis caused by Corynebacterium spp. is sometimes observed in patients with indwelling intravascular devices such as heart valves, shunts, or catheters.

One species, C. diptheriae, causes diptheria. Diphtheria is a highly infectious disease spread by direct physical contact or coughing and sneezing by infected persons. Diphtheria affects the upper respiratory tract with symptoms including sore throat, low-grade fever, headache, and the formation of a pseudomembrane on the tonsil(s), pharynx, and/or nose. C. diptheriae can also be found in skin lesions. If left untreated, the bacteria can produce toxins leading to complications like kidney damage, heart failure, and paralysis. Systematic vaccination in developed nations has effectively diminished the occurrence of what used to be a common disease. Thus, it would be very rare to find this particular species in the indoor environment.

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